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Nanoparticles are an indispensable part of our lives. From electronic devices to drug delivery to catalysis and energy storage, nanoparticles have found various important applications. Out of the many synthetic strategies to generate nanoparticles, electrodeposition has stood out due to its cost effectiveness, low time consumption and simplicity. However, traditional electrodeposition techniques have suffered from controlling the size, shape, morphology and microstructure of nanoparticles. Here, we use a technique called nanodroplet‐mediated electrodeposition, where nanodroplets carrying the metal salt precursor collide with a negatively‐biased electrode. In this work, we use this nanodroplet‐mediated electrodeposition technique along with transmission electron microscopy, selected‐area electron diffraction and high‐angle‐annular dark‐field scanning transmission electron microscopy to show control over the microstructure of single nanoparticles. Along with that, we use X‐ray photoelectron spectroscopy to get mechanistic insights behind the alteration of microstructure observed. Having achieved a control over the microstructure, we show the application by synthesising polycrystalline alloys at room temperature and evaluating the electrocatalytic behavior of the different microstructures towards the hydrogen evolution reaction. This fundamental work of controlling microstructures of single nanoparticles and its applications in alloy synthesis and electrocatalysis opens a new avenue of tuning nanoparticles for various applications.